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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 385 by tim, Tue Mar 1 20:10:14 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <cstring>
# Line 44 | Line 44
44   #include "primitives/DirectionalAtom.hpp"
45   #include "primitives/RigidBody.hpp"
46  
47 < namespace oopse {
48 < void BaseAtomVisitor::visit(RigidBody *rb) {
49 < //vector<Atom*> myAtoms;
50 < //vector<Atom*>::iterator atomIter;
47 > namespace OpenMD {
48 >  void BaseAtomVisitor::visit(RigidBody *rb) {
49 >    //vector<Atom*> myAtoms;
50 >    //vector<Atom*>::iterator atomIter;
51  
52 < //myAtoms = rb->getAtoms();
52 >    //myAtoms = rb->getAtoms();
53  
54 < //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55 < //  (*atomIter)->accept(this);
56 <    }
54 >    //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55 >    //  (*atomIter)->accept(this);
56 >  }
57  
58 < void BaseAtomVisitor::setVisited(Atom *atom) {
58 >  void BaseAtomVisitor::setVisited(Atom *atom) {
59      GenericData *data;
60      data = atom->getPropertyByName("VISITED");
61  
62      //if visited property is not existed, add it as new property
63      if (data == NULL) {
64 <        data = new GenericData();
65 <        data->setID("VISITED");
66 <        atom->addProperty(data);
64 >      data = new GenericData();
65 >      data->setID("VISITED");
66 >      atom->addProperty(data);
67      }
68 < }
68 >  }
69  
70 < bool BaseAtomVisitor::isVisited(Atom *atom) {
70 >  bool BaseAtomVisitor::isVisited(Atom *atom) {
71      GenericData *data;
72      data = atom->getPropertyByName("VISITED");
73      return data == NULL ? false : true;
74 < }
74 >  }
75  
76 < bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
76 >  bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
77      std::set<std::string>::iterator strIter;
78      strIter = ssdAtomType.find(atomType);
79      return strIter != ssdAtomType.end() ? true : false;
80 < }
80 >  }
81  
82 < void SSDAtomVisitor::visit(DirectionalAtom *datom) {
82 >  void SSDAtomVisitor::visit(DirectionalAtom *datom) {
83      std::vector<AtomInfo*>atoms;
84  
85 <    //we need to convert SSD into 4 differnet atoms
86 <    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
87 <    //of the water with a dipole moment
85 >    //we need to convert SSD into 4 different atoms
86 >    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of
87 >    //the mass of the water with a dipole moment
88      Vector3d h1(0.0, -0.75695, 0.5206);
89      Vector3d h2(0.0, 0.75695, 0.5206);
90      Vector3d ox(0.0, 0.0, -0.0654);
# Line 101 | Line 101 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
101  
102      //if atom is not SSD atom, just skip it
103      if (!isSSDAtom(datom->getType()))
104 <        return;
104 >      return;
105  
106      data = datom->getPropertyByName("ATOMDATA");
107  
108      if (data != NULL) {
109 <        atomData = dynamic_cast<AtomData *>(data);
109 >      atomData = dynamic_cast<AtomData *>(data);
110  
111 <        if (atomData == NULL) {
112 <            std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
113 <            atomData = new AtomData;
114 <            haveAtomData = false;
115 <        } else
116 <            haveAtomData = true;
111 >      if (atomData == NULL) {
112 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
113 >        atomData = new AtomData;
114 >        haveAtomData = false;
115 >      } else
116 >        haveAtomData = true;
117      } else {
118 <        atomData = new AtomData;
119 <        haveAtomData = false;
118 >      atomData = new AtomData;
119 >      haveAtomData = false;
120      }
121  
122      pos = datom->getPos();
# Line 132 | Line 132 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
132      newVec = rotTrans * u;
133  
134      atomInfo = new AtomInfo;
135 <    atomInfo->AtomType = "X";
135 >    atomInfo->atomTypeName = "X";
136      atomInfo->pos[0] = pos[0];
137      atomInfo->pos[1] = pos[1];
138      atomInfo->pos[2] = pos[2];
# Line 147 | Line 147 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
147      newVec = rotTrans * ox;
148  
149      atomInfo = new AtomInfo;
150 <    atomInfo->AtomType = "O";
150 >    atomInfo->atomTypeName = "O";
151      atomInfo->pos[0] = pos[0] + newVec[0];
152      atomInfo->pos[1] = pos[1] + newVec[1];
153      atomInfo->pos[2] = pos[2] + newVec[2];
# Line 160 | Line 160 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
160      //matVecMul3(rotTrans, h1, newVec);
161      newVec = rotTrans * h1;
162      atomInfo = new AtomInfo;
163 <    atomInfo->AtomType = "H";
163 >    atomInfo->atomTypeName = "H";
164      atomInfo->pos[0] = pos[0] + newVec[0];
165      atomInfo->pos[1] = pos[1] + newVec[1];
166      atomInfo->pos[2] = pos[2] + newVec[2];
# Line 173 | Line 173 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
173      //matVecMul3(rotTrans, h2, newVec);
174      newVec = rotTrans * h2;
175      atomInfo = new AtomInfo;
176 <    atomInfo->AtomType = "H";
176 >    atomInfo->atomTypeName = "H";
177      atomInfo->pos[0] = pos[0] + newVec[0];
178      atomInfo->pos[1] = pos[1] + newVec[1];
179      atomInfo->pos[2] = pos[2] + newVec[2];
# Line 185 | Line 185 | void SSDAtomVisitor::visit(DirectionalAtom *datom) {
185      //add atom data into atom's property
186  
187      if (!haveAtomData) {
188 <        atomData->setID("ATOMDATA");
189 <        datom->addProperty(atomData);
188 >      atomData->setID("ATOMDATA");
189 >      datom->addProperty(atomData);
190      }
191  
192      setVisited(datom);
193 < }
193 >  }
194  
195 < const std::string SSDAtomVisitor::toString() {
195 >  const std::string SSDAtomVisitor::toString() {
196      char   buffer[65535];
197      std::string result;
198  
# Line 212 | Line 212 | const std::string SSDAtomVisitor::toString() {
212      result += buffer;
213  
214      return result;
215 < }
215 >  }
216  
217 < bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
217 >
218 >  bool TREDAtomVisitor::isTREDAtom(const std::string&atomType) {
219      std::set<std::string>::iterator strIter;
220 +    strIter = tredAtomType.find(atomType);
221 +    return strIter != tredAtomType.end() ? true : false;
222 +  }
223 +
224 +  void TREDAtomVisitor::visit(DirectionalAtom *datom) {
225 +    std::vector<AtomInfo*>atoms;
226 +
227 +    // we need to convert a TRED into 4 different atoms:
228 +    // one oxygen atom, two hydrogen atoms, and one atom which is the center of
229 +    // the mass of the water with a dipole moment
230 +    Vector3d h1(0.0, -0.75695, 0.5206);
231 +    Vector3d h2(0.0, 0.75695, 0.5206);
232 +    Vector3d ox(0.0, 0.0, -0.0654);
233 +    Vector3d u(0, 0, 1);
234 +    RotMat3x3d   rotMatrix;
235 +    RotMat3x3d   rotTrans;
236 +    AtomInfo *   atomInfo;
237 +    Vector3d     pos;
238 +    Vector3d     newVec;
239 +    Quat4d       q;
240 +    AtomData *   atomData;
241 +    GenericData *data;
242 +    bool         haveAtomData;
243 +
244 +    // if the atom is not a TRED atom, skip it
245 +    if (!isTREDAtom(datom->getType()))
246 +      return;
247 +
248 +    data = datom->getPropertyByName("ATOMDATA");
249 +
250 +    if (data != NULL) {
251 +      atomData = dynamic_cast<AtomData *>(data);
252 +
253 +      if (atomData == NULL) {
254 +        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
255 +        atomData = new AtomData;
256 +        haveAtomData = false;
257 +      } else
258 +        haveAtomData = true;
259 +    } else {
260 +      atomData = new AtomData;
261 +      haveAtomData = false;
262 +    }
263 +
264 +    pos = datom->getPos();
265 +    q = datom->getQ();
266 +    rotMatrix = datom->getA();
267 +
268 +    // We need A^T to convert from body-fixed to space-fixed:
269 +    // transposeMat3(rotMatrix, rotTrans);
270 +    rotTrans = rotMatrix.transpose();
271 +
272 +    // center of mass of the water molecule
273 +    // matVecMul3(rotTrans, u, newVec);
274 +    newVec = rotTrans * u;
275 +
276 +    atomInfo = new AtomInfo;
277 +    atomInfo->atomTypeName = "TRED";
278 +    atomInfo->pos[0] = pos[0];
279 +    atomInfo->pos[1] = pos[1];
280 +    atomInfo->pos[2] = pos[2];
281 +    atomInfo->dipole[0] = newVec[0];
282 +    atomInfo->dipole[1] = newVec[1];
283 +    atomInfo->dipole[2] = newVec[2];
284 +
285 +    atomData->addAtomInfo(atomInfo);
286 +
287 +    // oxygen
288 +    // matVecMul3(rotTrans, ox, newVec);
289 +    newVec = rotTrans * ox;
290 +
291 +    atomInfo = new AtomInfo;
292 +    atomInfo->atomTypeName = "O";
293 +    atomInfo->pos[0] = pos[0] + newVec[0];
294 +    atomInfo->pos[1] = pos[1] + newVec[1];
295 +    atomInfo->pos[2] = pos[2] + newVec[2];
296 +    atomInfo->dipole[0] = 0.0;
297 +    atomInfo->dipole[1] = 0.0;
298 +    atomInfo->dipole[2] = 0.0;
299 +    atomData->addAtomInfo(atomInfo);
300 +
301 +    // hydrogen1
302 +    // matVecMul3(rotTrans, h1, newVec);
303 +    newVec = rotTrans * h1;
304 +    atomInfo = new AtomInfo;
305 +    atomInfo->atomTypeName = "H";
306 +    atomInfo->pos[0] = pos[0] + newVec[0];
307 +    atomInfo->pos[1] = pos[1] + newVec[1];
308 +    atomInfo->pos[2] = pos[2] + newVec[2];
309 +    atomInfo->dipole[0] = 0.0;
310 +    atomInfo->dipole[1] = 0.0;
311 +    atomInfo->dipole[2] = 0.0;
312 +    atomData->addAtomInfo(atomInfo);
313 +
314 +    // hydrogen2
315 +    // matVecMul3(rotTrans, h2, newVec);
316 +    newVec = rotTrans * h2;
317 +    atomInfo = new AtomInfo;
318 +    atomInfo->atomTypeName = "H";
319 +    atomInfo->pos[0] = pos[0] + newVec[0];
320 +    atomInfo->pos[1] = pos[1] + newVec[1];
321 +    atomInfo->pos[2] = pos[2] + newVec[2];
322 +    atomInfo->dipole[0] = 0.0;
323 +    atomInfo->dipole[1] = 0.0;
324 +    atomInfo->dipole[2] = 0.0;
325 +    atomData->addAtomInfo(atomInfo);
326 +
327 +    // add atom data into atom's property
328 +
329 +    if (!haveAtomData) {
330 +      atomData->setID("ATOMDATA");
331 +      datom->addProperty(atomData);
332 +    }
333 +
334 +    setVisited(datom);
335 +  }
336 +
337 +  const std::string TREDAtomVisitor::toString() {
338 +    char   buffer[65535];
339 +    std::string result;
340 +
341 +    sprintf(buffer,
342 +            "------------------------------------------------------------------\n");
343 +    result += buffer;
344 +
345 +    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
346 +    result += buffer;
347 +
348 +    sprintf(buffer,
349 +            "Visitor Description: Convert the TRED atom into 4 different atoms\n");
350 +    result += buffer;
351 +
352 +    sprintf(buffer,
353 +            "------------------------------------------------------------------\n");
354 +    result += buffer;
355 +
356 +    return result;
357 +  }
358 +
359 +
360 +  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
361 +    std::set<std::string>::iterator strIter;
362      strIter = linearAtomType.find(atomType);
363  
364      return strIter != linearAtomType.end() ? true : false;
365 < }
365 >  }
366  
367 < void LinearAtomVisitor::visit(DirectionalAtom* datom){
367 >  void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
368 >   linearAtomType.insert(atomType);
369 >  }
370 >
371 >  void LinearAtomVisitor::visit(DirectionalAtom* datom){
372      std::vector<AtomInfo*> atoms;
373      //we need to convert linear into 4 different atoms
374      Vector3d c1(0.0, 0.0, -1.8);
# Line 237 | Line 384 | void LinearAtomVisitor::visit(DirectionalAtom* datom){
384      AtomData* atomData;
385      GenericData* data;
386      bool haveAtomData;
387 +    //if atom is not linear atom, just skip it
388 +    if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
389 +      return;
390  
391 <    //if atom is not SSD atom, just skip it
392 <    if(!isLinearAtom(datom->getType()))
393 <        return;
391 >    //setup GayBerne type in fortran side
392 >    data = datom->getAtomType()->getPropertyByName("GayBerne");
393 >    if (data != NULL) {
394 >       GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
395  
396 +       if (gayBerneData != NULL) {
397 +           GayBerneParam gayBerneParam = gayBerneData->getData();
398 +
399 +                          // double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
400 +                          double halfLen = gayBerneParam.GB_l/2.0;
401 +                          c1[2] = -halfLen;
402 +              c2[2] = -halfLen /2;
403 +              c3[2] = halfLen/2;
404 +              c4[2] = halfLen;
405 +                
406 +            }
407 +            
408 +              else {
409 +                    sprintf( painCave.errMsg,
410 +                           "Can not cast GenericData to GayBerneParam\n");
411 +                    painCave.severity = OPENMD_ERROR;
412 +                    painCave.isFatal = 1;
413 +                    simError();          
414 +        }            
415 +    }
416 +
417 +
418      data = datom->getPropertyByName("ATOMDATA");
419      if(data != NULL){
420 <        atomData = dynamic_cast<AtomData*>(data);  
421 <        if(atomData == NULL){
422 <            std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
423 <            atomData = new AtomData;
424 <            haveAtomData = false;      
425 <        } else {
426 <            haveAtomData = true;
427 <        }
420 >      atomData = dynamic_cast<AtomData*>(data);  
421 >      if(atomData == NULL){
422 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
423 >        atomData = new AtomData;
424 >        haveAtomData = false;      
425 >      } else {
426 >        haveAtomData = true;
427 >      }
428      } else {
429 <        atomData = new AtomData;
430 <        haveAtomData = false;
429 >      atomData = new AtomData;
430 >      haveAtomData = false;
431      }
432    
433    
# Line 267 | Line 440 | void LinearAtomVisitor::visit(DirectionalAtom* datom){
440  
441      newVec = rotTrans * c1;
442      atomInfo = new AtomInfo;
443 <    atomInfo->AtomType = "C";
443 >    atomInfo->atomTypeName = "C";
444      atomInfo->pos[0] = pos[0] + newVec[0];
445      atomInfo->pos[1] = pos[1] + newVec[1];
446      atomInfo->pos[2] = pos[2] + newVec[2];
# Line 278 | Line 451 | void LinearAtomVisitor::visit(DirectionalAtom* datom){
451  
452      newVec = rotTrans * c2;
453      atomInfo = new AtomInfo;
454 <    atomInfo->AtomType = "C";
454 >    atomInfo->atomTypeName = "C";
455      atomInfo->pos[0] = pos[0] + newVec[0];
456      atomInfo->pos[1] = pos[1] + newVec[1];
457      atomInfo->pos[2] = pos[2] + newVec[2];
# Line 289 | Line 462 | void LinearAtomVisitor::visit(DirectionalAtom* datom){
462  
463      newVec = rotTrans * c3;
464      atomInfo = new AtomInfo;
465 <    atomInfo->AtomType = "C";
465 >    atomInfo->atomTypeName = "C";
466      atomInfo->pos[0] = pos[0] + newVec[0];
467      atomInfo->pos[1] = pos[1] + newVec[1];
468      atomInfo->pos[2] = pos[2] + newVec[2];
# Line 300 | Line 473 | void LinearAtomVisitor::visit(DirectionalAtom* datom){
473  
474      newVec = rotTrans * c4;
475      atomInfo = new AtomInfo;
476 <    atomInfo->AtomType = "C";
476 >    atomInfo->atomTypeName = "C";
477      atomInfo->pos[0] = pos[0] + newVec[0];
478      atomInfo->pos[1] = pos[1] + newVec[1];
479      atomInfo->pos[2] = pos[2] + newVec[2];
# Line 312 | Line 485 | void LinearAtomVisitor::visit(DirectionalAtom* datom){
485      //add atom data into atom's property
486  
487      if(!haveAtomData){
488 <        atomData->setID("ATOMDATA");
489 <        datom->addProperty(atomData);
488 >      atomData->setID("ATOMDATA");
489 >      datom->addProperty(atomData);
490      }
491  
492      setVisited(datom);
493  
494 < }
494 >  }
495  
496 < const std::string LinearAtomVisitor::toString(){
497 <  char buffer[65535];
498 <  std::string result;
496 >  const std::string LinearAtomVisitor::toString(){
497 >    char buffer[65535];
498 >    std::string result;
499    
500 <  sprintf(buffer ,"------------------------------------------------------------------\n");
501 <  result += buffer;
500 >    sprintf(buffer ,"------------------------------------------------------------------\n");
501 >    result += buffer;
502  
503 <  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
504 <  result += buffer;
503 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
504 >    result += buffer;
505  
506 <  sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
507 <  result += buffer;
506 >    sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
507 >    result += buffer;
508  
509 <  sprintf(buffer ,"------------------------------------------------------------------\n");
510 <  result += buffer;
509 >    sprintf(buffer ,"------------------------------------------------------------------\n");
510 >    result += buffer;
511  
512 <  return result;
513 < }
512 >    return result;
513 >  }
514  
515 < //----------------------------------------------------------------------------//
515 >  bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
516 >    std::set<std::string>::iterator strIter;
517 >    strIter = GBLipidAtomType.find(atomType);
518  
519 < void DefaultAtomVisitor::visit(Atom *atom) {
519 >    return strIter != GBLipidAtomType.end() ? true : false;
520 >  }
521 >
522 >  void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
523 >    std::vector<AtomInfo*> atoms;
524 >    Vector3d c1(0.0, 0.0, 0.0);
525 >    Vector3d c2(0.0, 0.0, 1.0);
526 >    RotMat3x3d rotMatrix;
527 >    RotMat3x3d rotTrans;
528 >    AtomInfo* atomInfo;
529 >    Vector3d pos;
530 >    Vector3d newVec;
531 >    Vector3d dVec;
532 >    Quat4d q;
533 >    AtomData* atomData;
534 >    GenericData* data;
535 >    bool haveAtomData;
536 >
537 >    //if atom is not GBlipid atom, just skip it
538 >    if(!isGBLipidAtom(datom->getType()))
539 >      return;
540 >
541 >    data = datom->getPropertyByName("ATOMDATA");
542 >    if(data != NULL){
543 >      atomData = dynamic_cast<AtomData*>(data);  
544 >      if(atomData == NULL){
545 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
546 >        atomData = new AtomData;
547 >        haveAtomData = false;      
548 >      } else {
549 >        haveAtomData = true;
550 >      }
551 >    } else {
552 >      atomData = new AtomData;
553 >      haveAtomData = false;
554 >    }
555 >  
556 >  
557 >    pos = datom->getPos();
558 >    q = datom->getQ();
559 >    rotMatrix = datom->getA();
560 >
561 >    // We need A^T to convert from body-fixed to space-fixed:  
562 >    rotTrans = rotMatrix.transpose();
563 >
564 >    newVec = rotTrans * c1;
565 >    dVec = rotTrans * c2;
566 >    atomInfo = new AtomInfo;
567 >    atomInfo->atomTypeName = "GB";
568 >    atomInfo->pos[0] = pos[0] + newVec[0];
569 >    atomInfo->pos[1] = pos[1] + newVec[1];
570 >    atomInfo->pos[2] = pos[2] + newVec[2];
571 >    atomInfo->dipole[0] = dVec[0];
572 >    atomInfo->dipole[1] = dVec[1];
573 >    atomInfo->dipole[2] = dVec[2];
574 >    atomInfo->hasVector = true;
575 >    atomInfo->charge = 3.0;
576 >    atomInfo->hasCharge = true;
577 >    atomData->addAtomInfo(atomInfo);
578 >
579 >    //add atom data into atom's property
580 >
581 >    if(!haveAtomData){
582 >      atomData->setID("ATOMDATA");
583 >      datom->addProperty(atomData);
584 >    }
585 >
586 >    setVisited(datom);
587 >
588 >  }
589 >
590 >  const std::string GBLipidAtomVisitor::toString(){
591 >    char buffer[65535];
592 >    std::string result;
593 >  
594 >    sprintf(buffer ,"------------------------------------------------------------------\n");
595 >    result += buffer;
596 >
597 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
598 >    result += buffer;
599 >
600 >    sprintf(buffer , "Visitor Description: Convert GBlipid into xyz-formatted atom for use with xyz2pov\n");
601 >    result += buffer;
602 >
603 >    sprintf(buffer ,"------------------------------------------------------------------\n");
604 >    result += buffer;
605 >
606 >    return result;
607 >  }
608 >
609 >  bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
610 >    std::set<std::string>::iterator strIter;
611 >    strIter = Ring5gbAtomType.find(atomType);
612 >
613 >    return strIter != Ring5gbAtomType.end() ? true : false;
614 >  }
615 >
616 >  void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
617 >    std::vector<AtomInfo*> atoms;
618 >    //we need to convert linear into 4 different atoms
619 >    Vector3d c1(0.0, 0.0, -5.5);
620 >    Vector3d c2(0.0, 0.0, -1.8);
621 >    Vector3d c3(0.0, 0.0,  1.8);
622 >    Vector3d c4(0.0, 0.0,  5.5);
623 >    RotMat3x3d rotMatrix;
624 >    RotMat3x3d rotTrans;
625 >    AtomInfo* atomInfo;
626 >    Vector3d pos;
627 >    Vector3d newVec;
628 >    Vector3d dVec;
629 >    Quat4d q;
630 >    AtomData* atomData;
631 >    GenericData* data;
632 >    bool haveAtomData;
633 >
634 >    //if atom is not Ring5GB atom, just skip it
635 >    if(!isRing5gbAtom(datom->getType()))
636 >      return;
637 >
638 >    data = datom->getPropertyByName("ATOMDATA");
639 >    if(data != NULL){
640 >      atomData = dynamic_cast<AtomData*>(data);  
641 >      if(atomData == NULL){
642 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
643 >        atomData = new AtomData;
644 >        haveAtomData = false;      
645 >      } else {
646 >        haveAtomData = true;
647 >      }
648 >    } else {
649 >      atomData = new AtomData;
650 >      haveAtomData = false;
651 >    }
652 >  
653 >  
654 >    pos = datom->getPos();
655 >    q = datom->getQ();
656 >    rotMatrix = datom->getA();
657 >
658 >    // We need A^T to convert from body-fixed to space-fixed:  
659 >    rotTrans = rotMatrix.transpose();
660 >
661 >    newVec = rotTrans * c1;
662 >    atomInfo = new AtomInfo;
663 >    atomInfo->atomTypeName = "K";
664 >    atomInfo->pos[0] = pos[0] + newVec[0];
665 >    atomInfo->pos[1] = pos[1] + newVec[1];
666 >    atomInfo->pos[2] = pos[2] + newVec[2];
667 >    atomInfo->dipole[0] = 0.0;
668 >    atomInfo->dipole[1] = 0.0;
669 >    atomInfo->dipole[2] = 0.0;
670 >    atomData->addAtomInfo(atomInfo);
671 >
672 >    newVec = rotTrans * c2;
673 >    atomInfo = new AtomInfo;
674 >    atomInfo->atomTypeName = "K";
675 >    atomInfo->pos[0] = pos[0] + newVec[0];
676 >    atomInfo->pos[1] = pos[1] + newVec[1];
677 >    atomInfo->pos[2] = pos[2] + newVec[2];
678 >    atomInfo->dipole[0] = 0.0;
679 >    atomInfo->dipole[1] = 0.0;
680 >    atomInfo->dipole[2] = 0.0;
681 >    atomData->addAtomInfo(atomInfo);
682 >
683 >    newVec = rotTrans * c3;
684 >    atomInfo = new AtomInfo;
685 >    atomInfo->atomTypeName = "K";
686 >    atomInfo->pos[0] = pos[0] + newVec[0];
687 >    atomInfo->pos[1] = pos[1] + newVec[1];
688 >    atomInfo->pos[2] = pos[2] + newVec[2];
689 >    atomInfo->dipole[0] = 0.0;
690 >    atomInfo->dipole[1] = 0.0;
691 >    atomInfo->dipole[2] = 0.0;
692 >    atomData->addAtomInfo(atomInfo);
693 >
694 >    newVec = rotTrans * c4;
695 >    atomInfo = new AtomInfo;
696 >    atomInfo->atomTypeName = "K";
697 >    atomInfo->pos[0] = pos[0] + newVec[0];
698 >    atomInfo->pos[1] = pos[1] + newVec[1];
699 >    atomInfo->pos[2] = pos[2] + newVec[2];
700 >    atomInfo->dipole[0] = 0.0;
701 >    atomInfo->dipole[1] = 0.0;
702 >    atomInfo->dipole[2] = 0.0;
703 >    atomData->addAtomInfo(atomInfo);
704 >
705 >    //add atom data into atom's property
706 >
707 >    if(!haveAtomData){
708 >      atomData->setID("ATOMDATA");
709 >      datom->addProperty(atomData);
710 >    }
711 >
712 >    setVisited(datom);
713 >
714 >  }
715 >
716 >  const std::string Ring5gbAtomVisitor::toString(){
717 >    char buffer[65535];
718 >    std::string result;
719 >  
720 >    sprintf(buffer ,"------------------------------------------------------------------\n");
721 >    result += buffer;
722 >
723 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
724 >    result += buffer;
725 >
726 >    sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
727 >    result += buffer;
728 >
729 >    sprintf(buffer ,"------------------------------------------------------------------\n");
730 >    result += buffer;
731 >
732 >    return result;
733 >  }
734 >
735 >  bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
736 >    std::set<std::string>::iterator strIter;
737 >    strIter = HeadAtomType.find(atomType);
738 >
739 >    return strIter != HeadAtomType.end() ? true : false;
740 >  }
741 >
742 >  void HeadAtomVisitor::visit(DirectionalAtom* datom){
743 >    std::vector<AtomInfo*> atoms;
744 >    //we need to convert linear into 2 different atoms
745 >    Vector3d c1(0.0, 0.0, -1.5);
746 >    Vector3d c2(0.0, 0.0, 1.5);
747 >    RotMat3x3d rotMatrix;
748 >    RotMat3x3d rotTrans;
749 >    AtomInfo* atomInfo;
750 >    Vector3d pos;
751 >    Vector3d newVec;
752 >    Vector3d dVec;
753 >    Quat4d q;
754 >    AtomData* atomData;
755 >    GenericData* data;
756 >    bool haveAtomData;
757 >
758 >    //if atom is not Head atom, just skip it
759 >    if(!isHeadAtom(datom->getType()))
760 >      return;
761 >
762 >    data = datom->getPropertyByName("ATOMDATA");
763 >    if(data != NULL){
764 >      atomData = dynamic_cast<AtomData*>(data);  
765 >      if(atomData == NULL){
766 >        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
767 >        atomData = new AtomData;
768 >        haveAtomData = false;      
769 >      } else {
770 >        haveAtomData = true;
771 >      }
772 >    } else {
773 >      atomData = new AtomData;
774 >      haveAtomData = false;
775 >    }
776 >  
777 >  
778 >    pos = datom->getPos();
779 >    q = datom->getQ();
780 >    rotMatrix = datom->getA();
781 >
782 >    // We need A^T to convert from body-fixed to space-fixed:  
783 >    rotTrans = rotMatrix.transpose();
784 >
785 >    newVec = rotTrans * c1;
786 >    atomInfo = new AtomInfo;
787 >    atomInfo->atomTypeName = "C";
788 >    atomInfo->pos[0] = pos[0] + newVec[0];
789 >    atomInfo->pos[1] = pos[1] + newVec[1];
790 >    atomInfo->pos[2] = pos[2] + newVec[2];
791 >    atomInfo->dipole[0] = 0.0;
792 >    atomInfo->dipole[1] = 0.0;
793 >    atomInfo->dipole[2] = 0.0;
794 >    atomData->addAtomInfo(atomInfo);
795 >
796 >    newVec = rotTrans * c2;
797 >    atomInfo = new AtomInfo;
798 >    atomInfo->atomTypeName = "O";
799 >    atomInfo->pos[0] = pos[0] + newVec[0];
800 >    atomInfo->pos[1] = pos[1] + newVec[1];
801 >    atomInfo->pos[2] = pos[2] + newVec[2];
802 >    atomInfo->dipole[0] = 0.0;
803 >    atomInfo->dipole[1] = 0.0;
804 >    atomInfo->dipole[2] = 0.0;
805 >    atomData->addAtomInfo(atomInfo);
806 >
807 >    //add atom data into atom's property
808 >
809 >    if(!haveAtomData){
810 >      atomData->setID("ATOMDATA");
811 >      datom->addProperty(atomData);
812 >    }
813 >
814 >    setVisited(datom);
815 >
816 >  }
817 >
818 >  const std::string HeadAtomVisitor::toString(){
819 >    char buffer[65535];
820 >    std::string result;
821 >  
822 >    sprintf(buffer ,"------------------------------------------------------------------\n");
823 >    result += buffer;
824 >
825 >    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
826 >    result += buffer;
827 >
828 >    sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
829 >    result += buffer;
830 >
831 >    sprintf(buffer ,"------------------------------------------------------------------\n");
832 >    result += buffer;
833 >
834 >    return result;
835 >  }
836 >
837 >
838 >  //----------------------------------------------------------------------------//
839 >
840 >  void DefaultAtomVisitor::visit(Atom *atom) {
841      AtomData *atomData;
842      AtomInfo *atomInfo;
843      Vector3d  pos;
844  
845      if (isVisited(atom))
846 <        return;
846 >      return;
847  
848      atomInfo = new AtomInfo;
849  
# Line 355 | Line 851 | void DefaultAtomVisitor::visit(Atom *atom) {
851      atomData->setID("ATOMDATA");
852  
853      pos = atom->getPos();
854 <    atomInfo->AtomType = atom->getType();
854 >    atomInfo->atomTypeName = atom->getType();
855      atomInfo->pos[0] = pos[0];
856      atomInfo->pos[1] = pos[1];
857      atomInfo->pos[2] = pos[2];
# Line 368 | Line 864 | void DefaultAtomVisitor::visit(Atom *atom) {
864      atom->addProperty(atomData);
865  
866      setVisited(atom);
867 < }
867 >  }
868  
869 < void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
869 >  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
870      AtomData *atomData;
871      AtomInfo *atomInfo;
872      Vector3d  pos;
873      Vector3d  u;
874  
875      if (isVisited(datom))
876 <        return;
876 >      return;
877  
878      pos = datom->getPos();
879 <    u = datom->getElectroFrame().getColumn(2);
880 <
879 >    if (datom->getAtomType()->isGayBerne()) {
880 >        u = datom->getA().transpose()*V3Z;        
881 >    } else if (datom->getAtomType()->isMultipole()) {
882 >        u = datom->getElectroFrame().getColumn(2);
883 >    }
884      atomData = new AtomData;
885      atomData->setID("ATOMDATA");
886      atomInfo = new AtomInfo;
887  
888 <    atomInfo->AtomType = datom->getType();
888 >    atomInfo->atomTypeName = datom->getType();
889      atomInfo->pos[0] = pos[0];
890      atomInfo->pos[1] = pos[1];
891      atomInfo->pos[2] = pos[2];
# Line 399 | Line 898 | void DefaultAtomVisitor::visit(DirectionalAtom *datom)
898      datom->addProperty(atomData);
899  
900      setVisited(datom);
901 < }
901 >  }
902  
903 < const std::string DefaultAtomVisitor::toString() {
903 >  const std::string DefaultAtomVisitor::toString() {
904      char   buffer[65535];
905      std::string result;
906  
# Line 421 | Line 920 | const std::string DefaultAtomVisitor::toString() {
920      result += buffer;
921  
922      return result;
923 < }
924 < } //namespace oopse
923 >  }
924 > } //namespace OpenMD

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